Find Bioconductor Packages

Update Installed Bioconductor Packages

Bioconductor packages, especially those in the development branch, are
updated fairly regularly. To identify packages requiring update within
your version of Bioconductor, start a new session of R and enter

source("http://bioconductor.org/biocLite.R")
biocLite() ## R version 3.0 or later

Use the argument ask=FALSE to update old packages without being
prompted. For older versions of R, use the command
biocLite(NULL). Read the help page for ?biocLite for additional
details.

Upgrading installed Bioconductor packages

Some versions of R support more than one version of Bioconductor. To
use the latest version of Bioconductor for your version of R, enter

source("http://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade") ## R version 2.15 or later

Read the help page for ?BiocUpgrade for additional details. Remember
that more recent versions of Bioconductor may be available if your
version of R is out-of-date.

Recompiling installed Bioconductor packages

Rarely, underlying changes in the operating system require ALL
installed packages to be recompiled for source (C or Fortran)
compatibility. One way to address this might be to start a new R
session and enter

As this will reinstall all currently installed packages, it likely
involves a significant amount of network bandwidth and compilation
time. All packages are implicitly updated, and the cumulative effect
might introduce wrinkles that disrupt your work flow. It also requires
that you have the necessary compilers installed.

Troubleshoot Package Installations

Use the commands

library(BiocInstaller)
biocValid() ## R version 3.0 or later

to flag packages that are either out-of-date or too new for your
version of Bioconductor. The output suggests ways to solve identified
problems, and the help page ?biocValid lists arguments influencing
the behavior of the function.

Why Use biocLite()?

biocLite() is the recommended way to install Bioconductor
packages. There are several reasons for preferring this to the
'standard' way in which R pacakges are installed via
install.packages().

Bioconductor has a repository and release schedule that differs from R
(Bioconductor has a 'devel' branch to which new packages and updates
are introduced, and a stable 'release' branch emitted once every 6
months to which bug fixes but not new features are introduced).

A consequence of the mismatch between R and Bioconductor release
schedules is that the Bioconductor version identified by
install.packages() is sometimes not the most recent 'release'
available. For instance, an R minor version may be introduced some
months before the next Bioc release. After the Bioc release the users
of the R minor version will be pointed to an out-of-date version of
Bioconductor.

A consequence of the distinct 'devel' branch is that
install.packages() sometimes points only to the 'release'
repository, whereas Bioconductor developers and users wanting
leading-edge features wish to access the Bioconductor 'devel'
repository. For instance, the Bioconductor 3.0 release is available
for R.3.1.x, so Bioconductor developers and leading-edge users need to
be able to install the devel version of Bioconductor packages into the
same version (though perhaps different instance or at least library
location) of R that supports version 2.14 of Bioconductor.

An indirect consequence of Bioconductor's structured release is that
packages generally have more extensive dependencies with one another,
both explicitly via the usual package mechanisms and implicitly
because the repository, release structure, and Bioconductor community
interactions favor re-use of data representations and analysis
concepts across packages. There is thus a higher premium on knowing
that packages are from the same release, and that all packages are
current within the release.

These days, the main purpose of
source("http://bioconductor.org/biocLite.R") is to install and
attach the 'BiocInstaller' package.

In a new installation, the script installs the most recent version of
the BiocInstaller package relevant to the version of R in use,
regardless of the relative times of R and Bioconductor release
cycles. The BiocInstaller package serves as the primary way to
identify the version of Bioconductor in use

> library(BiocInstaller)
Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help

Since new features are often appealing to users, but at the same time
require an updated version of Bioconductor, the source() command
evaluated in an out-of-date R will nudge users to upgrade, e.g., in
R-2.15.3

> source("http://bioconductor.org/biocLite.R")
A new version of Bioconductor is available after installing the most
recent version of R; see http://bioconductor.org/install

The biocLite() function is provided by BiocInstaller. This is a
wrapper around install.packages, but with the repository chosen
according to the version of Bioconductor in use, rather than to the
version relevant at the time of the release of R.

biocLite() also nudges users to remain current within a release, by
default checking for out-of-date packages and asking if the user would
like to update

(at some points in the R / Bioconductor release cycle use of 'devel'
requires use of a different version of R itself, in which case the
attempt to useDevel() fails with an appropriate message).

The BiocInstaller package also provides biocValid() to test that the
installed packages are not a hodgepodge from different Bioconductor
releases (the 'too new' packages have been installed from source
rather than a repository; regular users would seldom have these).